After missing two shooting opportunities and a free header at the end of the first half, Hasselbaink slotted in his first Buddies goal after 50 minutes following his summer move from relegated Hamilton.
Steven Thompson, who missed a penalty in the 0-0 draw at Dunfermline, had lofted a volley over and Gary Teale drilled an effort wide for the hosts, while the Dons had half chances through Josh Magennis and Scott Vernon but were distinctly second best.
St Mirren, with an unchanged starting XI, were full of energy and enthusiasm from the start, with Hasselbaink, nephew of former Holland striker Jimmy-Floyd Hasselbaink, a useful outlet.
After Clark Robertson was booked for a reckless lunge on Thompson after nine minutes, the striker went close to opening the scoring.
Thompson hit a side-foot volley over from six yards after Jeroen Tesselaar's corner had been headed back across a crowded box by Teale.
Hasselbaink shot over after a neat turn outside the box before Teale cut in from the right and fired a left-foot shot across goal.
Vernon became the second Aberdeen player booked for a foul on Saints midfield enforcer Jim Goodwin, who was later also shown a yellow card, before the visitors finally mustered a shot on target.
Magennis made space for himself 25 yards out and hit a low right-footed drive which Craig Samson gathered at the second attempt.
Hasselbaink continued to trouble the Dons and created space for himself on the edge of the area before firing narrowly wide.
Aberdeen were beginning to come into the game, but it was Saints who spurned the opportunity to take a half-time lead when the diminutive Hasselbaink missed a free header from Teale's cross.
Hasselbaink was in a more familiar position at the start of the second half and made a strong run down the left but his cross failed to find a team-mate.
The ball rebounded towards Paul McGowan, who hit a wild shot which appeared to strike Kari Arnason, but suggestions of handball were dismissed.
McGowan and Hasselbaink then combined to put Saints ahead.
Former Celtic youth player McGowan threaded a ball through to the onrushing Hasselbaink, who calmly tucked the ball low beyond Dons goalkeeper David Gonzalez.
McGowan was then booked for tangling with Mackie, who was also shown a yellow card, before Magennis was also cautioned and substituted soon after as the visitors' frustration began to tell.
Vernon had a header palmed around the post by Samson, but Saints regained composure and possession.
Dons boss Craig Brown had used all of his three substitutes with 16 minutes remaining, but still the visitors appeared devoid of ideas and a fresh impetus.
Saints remained in control and continued to try to build on their advantage, with Hasselbaink nipping through to dispossess Arnason, only for the defender's blushes to be saved by Gonzalez's speed off his line.
Substitute Michael Paton shot wide from 20 yards at the other end as the Dons came close to a leveller with five minutes remaining.
Hasselbaink was then given a rousing reception when he was replaced by Jon McShane.
Saints held out for all three points, but it could have been more comfortable as Gonzalez saved from substitute Graham Carey deep in stoppage time.